3N6X

Crystal structure of a Putative glutathionylspermidine synthase (Mfla_0391) from METHYLOBACILLUS FLAGELLATUS KT at 2.35 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb3N6X/pdb

• Classification: LIGASE
• Organism(s): Methylobacillus flagellatus KT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-26 Released: 2010-06-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Crystal structure of a Putative glutathionylspermidine synthase (Mfla_0391) from METHYLOBACILLUS FLAGELLATUS KT at 2.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.45 kDa 
• Atom Count: 3,903 
• Modelled Residue Count: 451 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathionylspermidine synthase	A	474	Methylobacillus flagellatus KT	Mutation(s): 0  Gene Names: Mfla_0391

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33N6X

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.344	α = 90
b = 97.344	β = 90
c = 155.487	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PHENIX	refinement
SOLVE	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations